"General purpose" control genes are important elements in
building complicated organisms like flies. Some "control" genes
are common to many organisms (they
are homologous
 inherited from our common ancestor). For example, Hox
genes help lay out the basic body forms of many animals, including
humans, flies, and worms. They set up the head-to-tail organization. You
can think of them as directing instructions as an embryo develops: "Put the
head here! Legs go over there!"

They are general purpose in the sense that they are similar in many organisms;
it doesn't matter if it's a mouse's head or a fly's head that is being
built, the same gene directs the process. Small changes in such powerful
regulatory genes, or changes in the genes turned on by them, could represent a major
source of evolutionary change.